feat: add sample data for hAdv-A

data/adenovirus/hadv-a/README.md

@@ -0,0 +1,23 @@
+# Human Adenovirus A (hAdv-A)
+
+https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=129875
+
+Initially contributed by [dnanto](https://github.com/nextstrain/nextclade/pull/673#issuecomment-1007488135)
+
+
+Run from project root as
+
+```bash
+nextalign \
+--verbose \
+--in-order \
+--sequences=data/adenovirus/hadv-a/sequences.fasta \
+--reference=data/adenovirus/hadv-a/reference.fasta \
+--genes=100K.1,12.5K.1,13.6K.1,13.6K.2,14.7K.1,19K.1,22K.1,33K.1,33K.2,34K.1,52K.1,55K.1,CR1-alpha.1,CR1-beta.1,DBP.1,E1A.1,E1A.2,II.1,III.1,IIIa.1,IV.1,IVa2.1,IX.1,ORF1.1,ORF2.1,ORF3.1,ORF4.1,ORF6slash7.1,ORF6slash7.2,RID-alpha.1,RID-beta.1,TP.1,TP.2,U.1,V.1,VI.1,VII.1,VIII.1,X.1,pol.1,pol.2,protease.1 \
+--genemap=data/adenovirus/hadv-a/genemap.gff \
+--nuc-seed-length=27 \
+--nuc-seed-spacing=10 \
+--max-indel=700 \
+--output-dir=tmp/ \
+--output-basename=nextalign
+```

data/adenovirus/hadv-a/genemap.gff

@@ -0,0 +1,45 @@
+##	Human	Adenovirus	A
+##sequence-region	NC_001460.1	1	34125
+##species	https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=129875
+NC_001460.1	RefSeq	gene	503	1069	.	+	0	gene_name=E1A.1
+NC_001460.1	RefSeq	gene	1145	1375	.	+	2	gene_name=E1A.2
+NC_001460.1	RefSeq	gene	1542	2033	.	+	0	gene_name=19K.1
+NC_001460.1	RefSeq	gene	1847	3295	.	+	0	gene_name=55K.1
+NC_001460.1	RefSeq	gene	3374	3808	.	+	0	gene_name=IX.1
+NC_001460.1	RefSeq	gene	13340	13348	.	-	0	gene_name=pol.1
+NC_001460.1	RefSeq	gene	4953	8513	.	-	0	gene_name=pol.2
+NC_001460.1	RefSeq	gene	13340	13348	.	-	0	gene_name=TP.1
+NC_001460.1	RefSeq	gene	8312	10228	.	-	0	gene_name=TP.2
+NC_001460.1	RefSeq	gene	3844	5202	.	-	0	gene_name=IVa2.1
+NC_001460.1	RefSeq	gene	29368	31131	.	+	0	gene_name=IV.1
+NC_001460.1	RefSeq	gene	22695	25043	.	+	0	gene_name=100K.1
+NC_001460.1	RefSeq	gene	24763	25077	.	+	0	gene_name=33K.1
+NC_001460.1	RefSeq	gene	25257	25556	.	+	2	gene_name=33K.2
+NC_001460.1	RefSeq	gene	24763	25311	.	+	0	gene_name=22K.1
+NC_001460.1	RefSeq	gene	25612	26313	.	+	0	gene_name=VIII.1
+NC_001460.1	RefSeq	gene	16843	17640	.	+	0	gene_name=VI.1
+NC_001460.1	RefSeq	gene	17740	20499	.	+	0	gene_name=II.1
+NC_001460.1	RefSeq	gene	20525	21145	.	+	0	gene_name=protease.1
+NC_001460.1	RefSeq	gene	13394	14887	.	+	0	gene_name=III.1
+NC_001460.1	RefSeq	gene	14902	15468	.	+	0	gene_name=VII.1
+NC_001460.1	RefSeq	gene	15509	16543	.	+	0	gene_name=V.1
+NC_001460.1	RefSeq	gene	16568	16786	.	+	0	gene_name=X.1
+NC_001460.1	RefSeq	gene	7731	8138	.	+	0	gene_name=13.6K.1
+NC_001460.1	RefSeq	gene	9370	9390	.	+	0	gene_name=13.6K.2
+NC_001460.1	RefSeq	gene	10428	11549	.	+	0	gene_name=52K.1
+NC_001460.1	RefSeq	gene	11570	13318	.	+	0	gene_name=IIIa.1
+NC_001460.1	RefSeq	gene	21215	22669	.	-	0	gene_name=DBP.1
+NC_001460.1	RefSeq	gene	26313	26630	.	+	0	gene_name=12.5K.1
+NC_001460.1	RefSeq	gene	26584	27378	.	+	0	gene_name=CR1-alpha.1
+NC_001460.1	RefSeq	gene	27381	28187	.	+	0	gene_name=CR1-beta.1
+NC_001460.1	RefSeq	gene	28207	28482	.	+	0	gene_name=RID-alpha.1
+NC_001460.1	RefSeq	gene	28479	28811	.	+	0	gene_name=RID-beta.1
+NC_001460.1	RefSeq	gene	28804	29190	.	+	0	gene_name=14.7K.1
+NC_001460.1	RefSeq	gene	29204	29356	.	-	0	gene_name=U.1
+NC_001460.1	RefSeq	gene	32168	32311	.	-	0	gene_name=ORF6slash7.1
+NC_001460.1	RefSeq	gene	31183	31416	.	-	0	gene_name=ORF6slash7.2
+NC_001460.1	RefSeq	gene	31436	32311	.	-	0	gene_name=34K.1
+NC_001460.1	RefSeq	gene	32244	32606	.	-	0	gene_name=ORF4.1
+NC_001460.1	RefSeq	gene	32613	32963	.	-	0	gene_name=ORF3.1
+NC_001460.1	RefSeq	gene	32960	33355	.	-	0	gene_name=ORF2.1
+NC_001460.1	RefSeq	gene	33387	33770	.	-	0	gene_name=ORF1.1